Parallel Processing Transport Model MT3DMS by Using OpenMP

Abstract

Solute transport modeling resolves advection, dispersion, and chemical reactions in groundwater systems with its accuracy depending on the resolution of domain at all scales, thus the computational efficiency of a simulator becomes a bottleneck for the wide application of numerical simulations. However, the traditional serial numerical simulators have reached their limits for the prohibitive computational time and memory requirement in solving large-scale problems. These limitations have greatly hindered the wide application of groundwater solute transport modeling. Thus, the development of an efficient method for handling large-scale groundwater solute transport simulation is urgently required. In this study, we developed and assessed a parallelized MT3DMS (Modular Three-Dimensional Multispecies Transport Model) by using OpenMP (Open specifications for Multi-Processing) to accelerate the solute transport simulation process. The parallelization was achieved by adding OpenMP compile directives (i.e., defining various types of parallel regions) into the most time-consuming packages, including the Advection package (ADV), Dispersion package (DSP), and Generalized Conjugate Gradient Solver package (GCG). This allows parallel processing on shared-memory multiprocessors, i.e., both the memory requirement and computing efforts are automatically distributed among all processors. Moreover, we discussed two different parallelization strategies for handling numerical models with either many layers or few layers. The performance of parallelized MT3DMS was assessed by two benchmark numerical models with different model domain sizes via a workstation with two quad-core processors. Results showed that the running time of parallelized MT3DMS can be 4.15 times faster than that using sequential MT3DMS. The effects of using different preconditioners (procedures that transform a given problem into a form that is more suitable for numerical solving methods) in the GCG package were additionally evaluated. The modified strategy for handling numerical models with few layers also achieved satisfactory results with running time two times faster than that via sequential simulation. Thus, the proposed parallelization allows high-resolution groundwater transport simulation with higher efficiency for large-scale or multimillion-cell simulation problems.

Improving the speed of global parallel optimization on PDE models with processor affinity scheduling

“…In the past, there have been studies reported on parallelizing the simulation computation of one value of X (parallelization inside 𝑆𝑖𝑚(𝑿)) using methods like domain decomposition (Hammond et al, 2014;Kamal & Adeli, 1990) or parallel execution of 𝑆𝑖𝑚(𝑿) at the do loop level (Huang et al, 2018). In the parallelize simulation case, multiple parallel processors are used to get one evaluation of 𝑆𝑖𝑚(𝑿) for only one set value of X.…”

“…The application of parallel processing on PDE-based analysis is mainly at two parallelization levels. One application level is aforementioned parallelized PDE simulation through domain partitioning tech-niques (Farhat et al, 1997;Hammond, et al, 2014;Kamal & Adeli, 1990;Wallin et al, 2004) or parallel execution at the do loop level (Huang et al, 2018). A parallelized PDE simulation can greatly reduce WCT either for analysis running a single simulation once or for iterative optimization analysis where a single PDE simulation needs to be solved iteratively (see examples in Adeli and Kamal (1992) and H. S. Park and Adeli (1997)).…”

Effects of Slip Length and Inertia on the Permeability of Fracture with Slippery Boundary Condition

“…Essentially, the fluid-borne contaminants travelling along with subsurface fluid flow are normally hard to predict, where non-Fickian transport phenomenon is pervasive [3,5]. In such a circumstance, a reliable characterization of subsurface flow fields is the key to accurately capture the transport process [12]. For fractures, although the traditional fracture flow theory, namely Cubic Law [13], or the recently modified Local Cubic Law considering fracture heterogeneity [14,15], have been widely used to predict fracture flow, how inertial effects come to play, and change fracture permeability remain less constraint.…”

Parallel Simulation in Subsurface Hydrology: Evaluating the Performance of Modeling Computers

“…Several studies have focused on parallelizing the simulation process, by rebuilding well documented and widely used software codes. Cheng et al (2014) developed a JASMIN‐based parallel computing implementation of Modflow, while Abdelaziz and Le (2014) and Huang et al (2018) developed parallelized versions of MT3DMS. Hammond et al (2014) evaluated the strong‐ and weak‐scaling parallel performance of PFLOTRAN, using four benchmarking simulations run on the Jaguar Cray XK6 supercomputer at Oak Ridge National Laboratory.…”